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[RESEARCH ARTICLE] pH Gradient Mitigation in the Leaf Cell Secretory Pathway Alters the Defense Response of Nicotiana benthamiana to Agroinfiltration Philippe V. Jutras, Frank Sainsbury, Marie-Claire Goulet, Pierre-Olivier Lavoie, Rachel Tardif, Louis-Philippe Hamel, Marc-André D’Aoust, and Dominique Michaud* * Corresponding author ([email protected]) SUPPLEMENTAL TABLES 1–9 PAGE 1 Supplemental Table S1 | Complete list of confidently identified proteins following iTRAQ analysis The complete list of proteins includes more than a thousand entries (see manuscript’s main text for more information on protein identification and selection in main dataset). Details for each entry are provided in Microsoft Excel document available online. PAGE 2 Supplemental Table S2 | The 60 most upregulated proteins in empty vector (EV)-infiltrated leaves relative to non-infiltrated leaves Accession Protein name Ratio P23432 Glucan endo-1,3-beta-glucosidase 21.52 J9XUY3 Kunitz-type protease inhibitor (Fragment) 15.24 K4B8W8 Phospholipase A1-IIgamma-like 9.57 Q50LG4 Suberization-associated anionic peroxidase-like 8.87 D4IHB9 Kunitz-type trypsin inhibitor alpha chain-like 8.15 Q84LQ7 29 kDa chitinase-like thermal hysteresis protein 7.37 A0A0B5GNH2 Endoplasmic reticulum chaperone binding protein 6.66 Q43584 Probable carboxylesterase 15 6.15 K4C2W4 Protein disulfide-isomerase 6.08 P08252 Endochitinase 4 6.02 P07052 Pathogenesis-related R major form 5.96 M1BBJ6 Probable mannitol dehydrogenase 5.60 Q9FR00 Calcium-binding CAST-like 5.47 Q9LW96 Inositol-3-phosphate synthase 5.07 Q2QFR3 Cysteine proteinase aleuran 4.96 Q70G33 Hydroxycinnamoyl quinate transferase 4.94 A0A059XN47 Polygalacturonase inhibitor protein 4.89 M1B584 DNA damage-inducible 1 4.88 Q9SSV1 Intracellular ribonuclease LX-like 4.64 K4B7Q7 Probable cinnamyl alcohol dehydrogenase 6 4.57 M1A9W5 Phosphoglycerate mutase family 4.51 U3PWQ0 Pathogen-related -like 4.36 A0A075EYT4 Peroxisomal acyl- oxidase 1A 4.29 F2VJF4 Miraculin-like protein 4.22 K4BRF6 Methyltransferase DDB_G0268948 4.19 Q6L5N5 Heat shock 70 kDa 17 4.15 M1AWJ2 Heat shock 70 (Hsp 70) family 4.10 Q03685 Luminal-binding protein 5 3.97 Q02200 Lignin-forming anionic peroxidase-like 3.94 PAGE 3 K4BF11 Peroxidase P7-like 3.91 C9DFB7 Protein disulfide isomerase 3.90 K4AR66 Peroxidase 2-like 3.86 V9TLJ9 12-oxophytodienoate reductase 1-like isoform X1 3.79 P80969 Tyramine N-feruloyltransferase 4 11-like 3.76 K4D1Z3 Pyruvate decarboxylase 1-like 3.69 K4CZD5 coatomer subunit delta-like 3.68 Q94KK8 Glutamate decarboxylase 4 3.67 P15797 Glucan endo-1,3-beta-glucosidase 3.60 Q03198 Proteinase inhibitor I-A 3.50 P14170 Osmotin 3.50 Q5NTA8 Putative 5-epi-aristolochene synthase 3.49 K4CGM9 Persulfide dioxygenase ETHE1 homolog, mitochondrial-like 3.49 K4BA67 Vacuolar-sorting receptor 6-like 3.33 Q43799 Apoplastic invertase 3.30 Q9XIY9 p27 precursor 3.24 M1CA03 psbP 1, chloroplastic 3.22 U3RJ91 Gamma aminobutyrate transaminase 3, chloroplastic 3.20 K4C735 2-alkenal reductase (NADP(+)-dependent) 3.11 K4C0M5 Carboxymethylenebutenolidase homolog 3.10 A0A0F6P9E3 Aldehyde dehydrogenase family 2 member C4 3.08 K4BT18 Uncharacterized protein 3.01 Q9SYX6 Glucan endo-1,3-beta-glucosidase 3.00 K4D5D7 LETM1 and EF-hand domain-containing 1, mitochondrial 2.99 M1CBR7 coatomer subunit delta-like 2.91 A0A068JKR2 Pathogenesis-related protein PR-10 2.90 M0ZX98 Subtilisin-like protease 2.89 K4C284 Glutamate decarboxylase-like 2.85 M1CL86 Dihydrolipoamide dehydrogenase precursor 2.84 P93344 Aldehyde dehydrogenase family 2 member B7-like 2.84 Q42964 Lignin-forming anionic peroxidase 2.81 PAGE 4 Supplemental Table S3 | The 60 most downregulated proteins in EV-infiltrated leaves relative to non-infiltrated leaves Accession Protein name Ratio K4CCP7 Elongation factor Ts 0.082 Q0PWS6 Chlorophyll a-b binding CP24 10A, chloroplastic 0.093 Q0PWS5 Chlorophyll a-b binding CP26, chloroplastic 0.095 Q43797 Pyrophosphate-energized vacuolar membrane proton pump 0.098 P59702 Photosystem II cytochrome b559 alpha subunit 0.098 A0A0A8WK76 Probable aquaporin PIP2-1 0.106 K4BKH7 Uncharacterized protein 0.106 Q40425 Glycine-rich RNA-binding -like 0.115 M1A0N1 Uncharacterized protein 0.118 K4C841 ACT domain-containing DS12, chloroplastic-like 0.123 K7WJR7 Chlorophyll a/b-binding protein 0.126 K4C4W2 Remorin a4-e8 0.127 P06290 ATP synthase CF0 subunit I (chloroplast) 0.128 I6N953 Photosystem II CP43 chlorophyll apo (chloroplast) 0.135 K4C7M7 ATP synthase subunit b , chloroplastic-like 0.141 P29302 Photosystem I reaction center subunit II, chloroplastic 0.143 M1DBW2 Ribosomal S12 (chloroplast) 0.144 M1A511 Photosystem I reaction center subunit N, chloroplastic 0.148 A0A075VUZ8 Photosystem II D2 (chloroplast) 0.151 Q84UU0 Photosystem I reaction center subunit XI, chloroplastic-like 0.152 K4CYL4 Cysteine synthase 1, mitochondrial 0.161 M1BRE6 rhodanese-like domain-containing 4, chloroplastic 0.165 A0A076L2F1 remorin 1 0.166 M1BAI7 Short-chain dehydrogenase TIC 32, chloroplastic-like 0.169 A8Y6H4 ATP synthase subunit beta (Fragment) 0.172 K4B0Q1 UPF0603 At1g54780, chloroplastic 0.175 K4AZT2 Curvature thylakoid 1A, chloroplastic 0.176 Q9XEX8 remorin 1 0.179 A7XZB8 Thylakoid formation 1, chloroplastic 0.180 PAGE 5 K4CRS9 Chlorophyll a-b binding , chloroplastic 0.184 G9BRR3 Heme oxygenase 1 0.196 Q84QE4 Thiamine thiazole synthase, chloroplastic 0.202 B5LAV6 Long chain acyl- synthetase 4-like 0.203 M1CRT2 Uncharacterized protein 0.205 A0A0C5B729 30S ribosomal protein S4, chloroplastic 0.208 P32980 ATP synthase delta chain, chloroplastic 0.209 K4B7F9 Uncharacterized protein 0.209 M1CCH8 Probable inactive serine threonine- kinase slob2 0.211 A0A0A1E5J9 Calcineurin B 3 0.218 A0A0C5AT01 Photosystem II protein D1 0.219 K4CHX2 Porphobilinogen deaminase, chloroplastic 0.220 A0A060B909 Cytochrome b6 0.221 A0A059Q6D7 Photosystem I P700 apo A2 (chloroplast) 0.232 M0ZH09 rhodanese-like domain-containing 4, chloroplastic 0.235 A0A060BCE9 Photosystem I P700 apo A1 (chloroplast) 0.239 M1DZ44 Photosystem II CP47 chlorophyll apo (chloroplast) 0.241 K4C390 Phosphomethylpyrimidine synthase, chloroplastic 0.241 K4ASB8 Uncharacterized protein 0.244 M1BIE3 Uncharacterized protein 0.249 Q08935 29 kDa ribonucleo A, chloroplastic 0.252 K4C994 beta-glucosidase 3B-like 0.252 M0ZU44 Elongation factor Ts isoform 2 0.259 K4BLP5 COBW domain-containing 1 0.260 K4BML2 30S ribosomal S17, chloroplastic 0.263 H1AD87 ADP-ribosylation factor 8A 0.268 B3F8G9 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 0.270 K4BPJ2 Actin-depolymerizing factor 2 0.270 K4CXU8 Chlorophyll a-b binding 8, chloroplastic-like 0.273 H9CCH7 3-oxoacyl-[acyl-carrier- ] reductase 4-like 0.275 K4BXD1 30S ribosomal 3, chloroplastic-like 0.278 PAGE 6 Supplemental Table S4 | The 60 most upregulated proteins in M2-expressing leaves relative to EV-infiltrated leaves Accession Protein name Ratio M1DBW2 Ribosomal S12 (chloroplast) 2.58 M1A0N1 Uncharacterized protein 2.34 K4BLP5 COBW domain-containing 1 2.31 Q40425 Glycine-rich RNA-binding-like 2.28 K4CCP7 Elongation factor Ts 2.27 H2ESL0 Pathogenesis-related protein PR10 2.23 A0A088DBC4 Copper transport ATX1-like 2.16 K4CYL4 Cysteine synthase 1 2.11 A0A0C5B729 30S ribosomal protein S4 2.08 M1B359 Probable NAD(P)H dehydrogenase (quinone) FQR1-like 1 2.04 K4C4W2 Remorin 1 1.98 Q36570 Ribosomal S19 (chloroplast) 1.94 K4BF11 Peroxidase P7-like 1.93 A0A068JKR2 Pathogenesis-related protein PR-10 1.91 Q84QE4 Thiamine thiazole synthase, chloroplastic 1.89 M1D6E8 Ribulose bisphosphate carboxylase oxygenase large subunit 1.87 K4CHX2 Porphobilinogen deaminase, chloroplastic 1.85 Q2EZ42 Ribulose bisphosphate carboxylase/oxygenase large subunit 1.83 K4C390 Phosphomethylpyrimidine synthase, chloroplastic 1.82 P30155 50S ribosomal L27, chloroplastic 1.82 A0A076FNJ9 Delta-aminolevulinic acid dehydratase, chloroplastic 1.75 M1A047 Huntingtin-interacting K 1.74 K4BV58 30S ribosomal S9, chloroplastic 1.74 K4C841 ACT domain-containing DS12, chloroplastic-like isoform X1 1.73 K4BML2 30S ribosomal S17, chloroplastic 1.72 K4DI37 50S ribosomal L6, chloroplastic 1.71 Q7YM65 Ribulose bisphosphate carboxylase large chain (Fragment) 1.71 E5FE88 Ribulose bisphosphate/carboxylase large subunit (Fragment) 1.69 K4DHX8 Heat shock factor-binding 1-like 1.68 PAGE 7 Q40893 Ribulose 1,5-bisphosphate carboxylase small subunit mRNA 1.67 M1A989 50S ribosomal L1, chloroplastic 1.66 M0ZY56 Plasma membrane ATPase 4 1.64 K4B9S5 ATP synthase gamma chain, chloroplastic 1.63 Q8S8W8 ATP synthase CF1 beta subunit (chloroplast) 1.63 A8Y6H4 ATP synthase subunit beta (Fragment) 1.61 M1BZW7 transketolase, chloroplastic 1.61 K4C7M7 ATP synthase subunit b , chloroplastic 1.60 K4C261 Serine hydroxymethyltransferase 4 1.59 A5A5A1 50S ribosomal L25 1.59 Q0PWS6 Chlorophyll a-b binding CP24 10A, chloroplastic 1.58 K4BG20 60S ribosomal L26-1 1.57 A0A076KWG9 Sedoheptulose-1,7-bisphosphatase, chloroplastic 1.54 K4BKH7 Uncharacterized protein 1.54 K4CNG0 50S ribosomal L19-2, chloroplastic-like 1.54 M1C888 Thioredoxin Y1, chloroplastic 1.53 M1C9L0 HIPL1 -like 1.52 K4BVS6 Thioredoxin CDSP32, chloroplastic 1.52 K4D5C2 Phosphoglycolate phosphatase 1B, chloroplastic-like 1.52 C3RXI5 Plastid transketolase 1.51 M0ZH09 Rhodanese-like domain-containing 4, chloroplastic 1.51 M1B9T8 Aspartate aminotransferase, cytoplasmic 1.51 K4BIC8 Probable calcium-binding CML13 1.51 K4BXD1 30S ribosomal 3, chloroplastic-like 1.50 S5ZIN5 Cysteine synthase 1.49 K4CR71 Actin-depolymerizing factor 1 1.48 M1BQT9 DJ-1 homolog D 1.48 M1BTP6 14-3-3 9 1.48 A0A059Q659 Ribosomal protein S8 1.48
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    (19) & (11) EP 2 084 519 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: G01N 23/223 (2006.01) G01T 1/36 (2006.01) 01.08.2012 Bulletin 2012/31 C12Q 1/00 (2006.01) (21) Application number: 07874491.9 (86) International application number: PCT/US2007/021888 (22) Date of filing: 10.10.2007 (87) International publication number: WO 2008/127291 (23.10.2008 Gazette 2008/43) (54) X-RAY FLUORESCENCE ANALYSIS METHOD RÖNTGENFLUORESZENZ-ANALYSEVERFAHREN PROCÉDÉ D’ANALYSE PAR RAYONS X FLUORESCENTS (84) Designated Contracting States: • BURRELL, Anthony, K. AT BE BG CH CY CZ DE DK EE ES FI FR GB GR Los Alamos, NM 87544 (US) HU IE IS IT LI LT LU LV MC MT NL PL PT RO SE SI SK TR (74) Representative: Albrecht, Thomas Kraus & Weisert (30) Priority: 10.10.2006 US 850594 P Patent- und Rechtsanwälte Thomas-Wimmer-Ring 15 (43) Date of publication of application: 80539 München (DE) 05.08.2009 Bulletin 2009/32 (56) References cited: (60) Divisional application: JP-A- 2001 289 802 US-A1- 2003 027 129 12164870.3 US-A1- 2003 027 129 US-A1- 2004 004 183 US-A1- 2004 017 884 US-A1- 2004 017 884 (73) Proprietors: US-A1- 2004 093 526 US-A1- 2004 235 059 • Los Alamos National Security, LLC US-A1- 2004 235 059 US-A1- 2005 011 818 Los Alamos, NM 87545 (US) US-A1- 2005 011 818 US-B1- 6 329 209 • Caldera Pharmaceuticals, INC. US-B2- 6 719 147 Los Alamos, NM 87544 (US) • GOLDIN E M ET AL: "Quantitation of antibody (72) Inventors: binding to cell surface antigens by X-ray • BIRNBAUM, Eva, R.